101,151 research outputs found
Sorted Consecutive Occurrence Queries in Substrings
No full textThe string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for preprocessing and a pattern P of length m as a query, the goal is to report all occurrences of P as substrings of T. Navarro and Thankachan [CPM 2015, Theor. Comput. Sci. 2016] introduced a variant of this problem called the gap-bounded consecutive occurrence query, which reports pairs of consecutive occurrences of P in T such that their gaps (i.e., the distances between them) lie within a query-specified range [g₁, g₂]. Recently, Bille et al. [FSTTCS 2020, Theor. Comput. Sci. 2022] proposed the top-k close consecutive occurrence query, which reports the k closest consecutive occurrences of P in T, sorted in non-decreasing order of distance. Both problems are optimally solved in query time with O(n log n)-space data structures.
In this paper, we generalize these problems to the range query model, which focuses only on occurrences of P in a specified substring T[a.. b] of T. Our contributions are as follows:
- We propose an O(n log² n)-space data structure that answers the range top-k consecutive occurrence query in O(|P| + log log n + k) time.
- We propose an O(n log^{2+ε} n)-space data structure that answers the range gap-bounded consecutive occurrence query in O(|P| + log log n + output) time, where ε is a positive constant and output denotes the number of outputs. Additionally, as by-products, we present algorithms for geometric problems involving weighted horizontal segments in a 2D plane, which are of independent interest
Letter, [Author unclear] to Paulina T. Merritt
No full textHandwritten letter to Paulina Merritt from an unknown author, October 1, 1876.
Applying polynomial filtering to mass preconditioned Hybrid Monte Carlo
No full textAbstract not availableTaylor Haar, Waseem Kamleh, James Zanotti, Yoshifumi Nakamur
On Polynomial Time Constructions of Minimum Height Decision Tree
No full textA decision tree T in B_m:={0,1}^m is a binary tree where each of its internal nodes is labeled with an integer in [m]={1,2,...,m}, each leaf is labeled with an assignment a in B_m and each internal node has two outgoing edges that are labeled with 0 and 1, respectively. Let A subset {0,1}^m. We say that T is a decision tree for A if (1) For every a in A there is one leaf of T that is labeled with a. (2) For every path from the root to a leaf with internal nodes labeled with i_1,i_2,...,i_k in[m], a leaf labeled with a in A and edges labeled with xi_{i_1},...,xi_{i_k}in {0,1}, a is the only element in A that satisfies a_{i_j}=xi_{i_j} for all j=1,...,k.
Our goal is to write a polynomial time (in n:=|A| and m) algorithm that for an input A subseteq B_m outputs a decision tree for A of minimum depth. This problem has many applications that include, to name a few, computer vision, group testing, exact learning from membership queries and game theory.
Arkin et al. and Moshkov [Esther M. Arkin et al., 1998; Mikhail Ju. Moshkov, 2004] gave a polynomial time (ln |A|)- approximation algorithm (for the depth). The result of Dinur and Steurer [Irit Dinur and David Steurer, 2014] for set cover implies that this problem cannot be approximated with ratio (1-o(1))* ln |A|, unless P=NP. Moshkov studied in [Mikhail Ju. Moshkov, 2004; Mikhail Ju. Moshkov, 1982; Mikhail Ju. Moshkov, 1982] the combinatorial measure of extended teaching dimension of A, ETD(A). He showed that ETD(A) is a lower bound for the depth of the decision tree for A and then gave an exponential time ETD(A)/log(ETD(A))-approximation algorithm and a polynomial time 2(ln 2)ETD(A)-approximation algorithm.
In this paper we further study the ETD(A) measure and a new combinatorial measure, DEN(A), that we call the density of the set A. We show that DEN(A) <=ETD(A)+1. We then give two results. The first result is that the lower bound ETD(A) of Moshkov for the depth of the decision tree for A is greater than the bounds that are obtained by the classical technique used in the literature. The second result is a polynomial time (ln 2)DEN(A)-approximation (and therefore (ln 2)ETD(A)-approximation) algorithm for the depth of the decision tree of A.
We then apply the above results to learning the class of disjunctions of predicates from membership queries [Nader H. Bshouty et al., 2017]. We show that the ETD of this class is bounded from above by the degree d of its Hasse diagram. We then show that Moshkov algorithm can be run in polynomial time and is (d/log d)-approximation algorithm. This gives optimal algorithms when the degree is constant. For example, learning axis parallel rays over constant dimension space
Handwritten biographical information on Paulina T. McClung Merritt
No full textA handwritten biography of Paulina T. McClung Merritt by an unknown author, 1892.
Heterogeneous and tissue-specific regulation of effector T cell responses by IFN-gamma during Plasmodium berghei ANKA infection.
No full textIFN-γ and T cells are both required for the development of experimental cerebral malaria during Plasmodium berghei ANKA infection. Surprisingly, however, the role of IFN-γ in shaping the effector CD4(+) and CD8(+) T cell response during this infection has not been examined in detail. To address this, we have compared the effector T cell responses in wild-type and IFN-γ(-/-) mice during P. berghei ANKA infection. The expansion of splenic CD4(+) and CD8(+) T cells during P. berghei ANKA infection was unaffected by the absence of IFN-γ, but the contraction phase of the T cell response was significantly attenuated. Splenic T cell activation and effector function were essentially normal in IFN-γ(-/-) mice; however, the migration to, and accumulation of, effector CD4(+) and CD8(+) T cells in the lung, liver, and brain was altered in IFN-γ(-/-) mice. Interestingly, activation and accumulation of T cells in various nonlymphoid organs was differently affected by lack of IFN-γ, suggesting that IFN-γ influences T cell effector function to varying levels in different anatomical locations. Importantly, control of splenic T cell numbers during P. berghei ANKA infection depended on active IFN-γ-dependent environmental signals--leading to T cell apoptosis--rather than upon intrinsic alterations in T cell programming. To our knowledge, this is the first study to fully investigate the role of IFN-γ in modulating T cell function during P. berghei ANKA infection and reveals that IFN-γ is required for efficient contraction of the pool of activated T cells
Dispelling the Myths Behind First-author Citation Counts
No full textWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Two mechanisms regulate keratin K15 expression in keratinocytes:role of PKC/AP-1 and FOXM1 mediated signalling
No full textBackground: Keratin 15 (K15) is a type I keratin that is used as a marker of stem cells. Its expression is restricted to the basal layer of stratified epithelia, and the bulge in hair follicles. However, in certain clinical situations including oral lichen planus, K15 is induced in suprabasal layers, which is inconsistent with the role of a stem cell marker. This study provides insights into the mechanisms of K15 expression in the basal and differentiating keratinocytes. Methodology/Principal Findings: Human keratinocytes were differentiated by three different methods; suspension in methylcellulose, high cell density and treatment with phorbol ester. The expression of mRNA was determined by quantitative PCR and protein by western blotting and immunostaining. Keratinocytes in suspension suppressed ß1-integrin expression, induced differentiation-specific markers and K15, whereas FOXM1 (a cell cycle regulated protein) and K14 were downregulated. Rescuing ß1-integrin by either fibronectin or the arginine-glycine-aspartate peptide suppressed K15 but induced K14 and FOXM1 expression. Specific inhibition of PKCd, by siRNA, and AP-1 transcription factor, by TAM67 (dominant negative c-Jun), suppressed K15 expression, suggesting that PKC/AP-1 pathway plays a role in the differentiation-specific expression of K15. The basal cell-specific K15 expression may involve FOXM1 because ectopic expression of the latter is known to induce K15. Using chromatin immunoprecipitation, we have identified a single FOXM1 binding motif in the K15 promoter. Conclusions/Significance: The data suggests that K15 is induced during terminal differentiation mediated by the down regulation of ß1-integrin. However, this cannot be the mechanism of basal/stem cell-specific K15 expression in stratified epithelia, because basal keratinocytes do not undergo terminal differentiation. We propose that there are two mechanisms regulating K15 expression in stratified epithelia; differentiation-specific involving PKC/AP-1 pathway, and basal-specific mediated by FOXM1, and therefore the use of K15 expression as a marker of stem cells must be viewed with caution
Pelevin’s Trinity in the novel “t”: author – protagonist – reader
No full textThe article attempts to interpret Pelevin's artistic strategy in the novel "T" by exploring its subject organization and addressing the key problems of the author, the protagonist, and the reader as they are seen by the researcher. The article analyzes the peculiarities of constructing the narrative reality in the novel "T", and goes on to discuss Pelevin's philosophic models of the development of the humankind, and the emergence of his new anthropology
Measuring industry-science links through inventor-author relations: A profiling method
No full textIn this pilot study we examine the performance of text-based profiling in recovering a set of validated inventor-author links. In a first step we match patents and publications solely based on their similarity in content. Next, we compare inventor and author names on the highest ranked matches for the occurrence of name matches. Finally, we compare these candidate matches with the names listed in a validated set of inventor-author names. Our text-based profile methodology performs significantly better than a random matching of patents and publications, suggesting that text-based profiling is a valuable complementary tool to the name searches used in previous studies.innovation; industry-science links; text-based profiling;
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